Biomarker Discovery

Umeda M, Ma J, Huang BJ, Hagiwara K, Westover T, Abdelhamed S, Barajas JM, Thomas ME, Walsh MP, Song G, Tian L, Liu Y, Chen X, Kolekar P, Tran Q, Foy SG, Maciaszek JL, Kleist AB, Leonti AR, Ju B, Easton J, Wu H, Valentine V, Valentine MB, Liu YC, Ries RE, Smith JL, Parganas E, Iacobucci I, Hiltenbrand R, Miller J, Myers JR, Rampersaud E, Rahbarinia D, Rusch M, Wu G, Inaba H, Wang YC, Alonzo TA, Downing JR, Mullighan CG, Pounds S, Babu MM, Zhang J, Rubnitz JE, Meshinchi S, Ma X, Klco JM. Integrated genomic analysis identifies UBTF tandem duplications as a recurrent lesion in pediatric acute myeloid leukemia. Blood Cancer Discov. 2022 Feb 16:bloodcandisc.BCD-21-0160-A.2021. doi: 10.1158/2643-3230.BCD-21-0160. Epub ahead of print. PMID: 35176137.

Lamble AJ, Eidenschink Brodersen L, Alonzo TA, Wang J, Pardo L, Sung L, Cooper TM, Kolb EA, Aplenc R, Tasian SK, Loken MR, Meshinchi S. CD123 Expression Is Associated With High-Risk Disease Characteristics in Childhood Acute Myeloid Leukemia: A Report From the Children's Oncology Group. J Clin Oncol. 2022 Jan 20;40(3):252-261. doi: 10.1200/JCO.21.01595. Epub 2021 Dec 2. PMID: 34855461; PMCID: PMC8769096.

Bolouri H, Ries R, Pardo L, Hylkema T, Zhou W, Smith JL, Leonti A, Loken M, Farrar JE, Triche TJ Jr, Meshinchi S. A B-cell developmental gene regulatory network is activated in infant AML. PLoS One. 2021 Nov 18;16(11):e0259197. doi: 10.1371/journal.pone.0259197. PMID: 34793513; PMCID: PMC8601427.

Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia. Nat Genet. 2021 Nov;53(11):1586-1596. doi: 10.1038/s41588-021-00941-9. Epub 2021 Oct 18. PMID: 34663924; PMCID: PMC8571097.

Huang BJ, Smith JL, Wang YC, Taghizadeh K, Leonti AR, Ries RE, Liu Y, Kolekar P, Tarlock K, Gerbing R, Crowgey E, Furlan SN, Shaw TI, Hagiwara K, Wei L, Cooper TM, Gamis AS, Aplenc R, Kolb EA, Farrar JE, Triche T, Alonzo TA, Ma X, Meshinchi S. CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Adv. 2021 Dec 14;5(23):4963-4968. doi: 10.1182/bloodadvances.2021004965. PMID: 34547772.

Tarlock K, Lamble AJ, Wang YC, Gerbing RB, Ries RE, Loken MR, Brodersen LE, Pardo L, Leonti A, Smith JL, Hylkema TA, Woods WG, Cooper TM, Kolb EA, Gamis AS, Aplenc R, Alonzo TA, Meshinchi S. CEBPA-bZip mutations are associated with favorable prognosis in de novo AML: a report from the Children's Oncology Group. Blood. 2021 Sep 30;138(13):1137-1147. doi: 10.1182/blood.2020009652. Erratum in: Blood. 2022 Mar 10;139(10):1601. PMID: 33951732; PMCID: PMC8570058.

Tarlock K, Alonzo T, Wang YC, Gerbing RB, Ries RE, Hylkema T, Smith JL, Maxson JE, Meshinchi S. Prognostic impact of CSF3R mutations in favorable risk childhood acute myeloid leukemia. Blood. 2020 Apr 30;135(18):1603-1606. doi: 10.1182/blood.2019004179. PMID: 32187354; PMCID: PMC7193184.

Tarlock K, Alonzo TA, Wang YC, Gerbing RB, Ries R, Loken MR, Pardo L, Hylkema T, Joaquin J, Sarukkai L, Raimondi SC, Hirsch B, Sung L, Aplenc R, Bernstein I, Gamis AS, Meshinchi S, Pollard JA. Functional Properties of KIT Mutations Are Associated with Differential Clinical Outcomes and Response to Targeted Therapeutics in CBF Acute Myeloid Leukemia. Clin Cancer Res. 2019 Aug 15;25(16):5038-5048. doi: 10.1158/1078-0432.CCR-18-1897. Epub 2019 Jun 10. PMID: 31182436; PMCID: PMC6754181.

Therapeutic Targets

Gopalakrishnapillai A, Correnti CE, Pilat K, Lin I, Chan MK, Bandaranayake AD, Mehlin C, Kisielewski A, Hamill D, Kaeding AJ, Meshinchi S, Olson JM, Kolb EA, Barwe SP. Immunotherapeutic Targeting of Mesothelin Positive Pediatric AML Using Bispecific T Cell Engaging Antibodies. Cancers (Basel). 2021 Nov 26;13(23):5964. doi: 10.3390/cancers13235964. PMID: 34885074; PMCID: PMC8657033.

Le Q, Castro S, Tang T, Loeb AM, Hylkema T, McKay CN, Perkins L, Srivastava S, Call L, Smith J, Leonti A, Ries R, Pardo L, Loken MR, Correnti C, Fiorenza S, Turtle CJ, Riddell S, Tarlock K, Meshinchi S. Therapeutic Targeting of Mesothelin with Chimeric Antigen Receptor T Cells in Acute Myeloid Leukemia. Clin Cancer Res. 2021 Oct 15;27(20):5718-5730. doi: 10.1158/1078-0432.CCR-21-1546. Epub 2021 Aug 11. PMID: 34380639.

Kaeding AJ, Barwe SP, Gopalakrishnapillai A, Ries RE, Alonzo TA, Gerbing RB, Correnti C, Loken MR, Broderson LE, Pardo L, Le QH, Tang T, Leonti AR, Smith JL, Chou CK, Xu M, Triche T, Kornblau SM, Kolb EA, Tarlock K, Meshinchi S. Mesothelin is a novel cell surface disease marker and potential therapeutic target in acute myeloid leukemia. Blood Adv. 2021 May 11;5(9):2350-2361. doi: 10.1182/bloodadvances.2021004424. PMID: 33938941; PMCID: PMC8114558.

Gbadamosi MO, Shastri VM, Hylkema T, Papageorgiou I, Pardo L, Cogle CR, Doty A, Loken MR, Meshinchi S, Lamba JK. Novel CD33 antibodies unravel localization, biology and therapeutic implications of CD33 isoforms. Future Oncol. 2021 Jan;17(3):263-277. doi: 10.2217/fon-2020-0746. Epub 2020 Dec 24. PMID: 33356566.

Biernacki MA, Foster KA, Woodward KB, Coon ME, Cummings C, Cunningham TM, Dossa RG, Brault M, Stokke J, Olsen TM, Gardner K, Estey E, Meshinchi S, Rongvaux A, Bleakley M. CBFB-MYH11 fusion neoantigen enables T cell recognition and killing of acute myeloid leukemia. J Clin Invest. 2020 Oct 1;130(10):5127-5141. doi: 10.1172/JCI137723. PMID: 32831296; PMCID: PMC7524498.

Other Research

Pollard JA, Alonzo TA, Gerbing R, Brown P, Fox E, Choi J, Fisher B, Hirsch B, Kahwash S, Getz K, Levine J, Brodersen LE, Loken MR, Raimondi S, Tarlock K, Wood A, Sung L, Kolb EA, Gamis A, Meshinchi S, Aplenc R. Sorafenib in Combination With Standard Chemotherapy for Children With High Allelic Ratio FLT3/ITD+ Acute Myeloid Leukemia: A Report From the Children's Oncology Group Protocol AAML1031. J Clin Oncol. 2022 Mar 29:JCO2101612. doi: 10.1200/JCO.21.01612. Epub ahead of print. PMID: 35349331.

Chisholm KM, Heerema-McKenney AE, Choi JK, Smith J, Ries RE, Hirsch BA, Raimondi SC, Alonzo TA, Wang YC, Aplenc R, Sung L, Gamis AS, Meshinchi S, Kahwash SB. Acute erythroid leukemia is enriched in NUP98 fusions: a report from the Children's Oncology Group. Blood Adv. 2020 Dec 8;4(23):6000-6008. doi: 10.1182/bloodadvances.2020002712. PMID: 33284945; PMCID: PMC7724911.

Noort S, Wander P, Alonzo TA, Smith J, Ries RE, Gerbing RB, Dolman MEM, Locatelli F, Reinhardt D, Baruchel A, Stary J, Molenaar JJ, Stam RW, van den Heuvel-Eibrink MM, Zwaan MC, Meshinchi S. The clinical and biological characteristics of NUP98-KDM5A in pediatric acute myeloid leukemia. Haematologica. 2021 Feb 1;106(2):630-634. doi: 10.3324/haematol.2019.236745. PMID: 32381579; PMCID: PMC7849578.

Aplenc R, Meshinchi S, Sung L, Alonzo T, Choi J, Fisher B, Gerbing R, Hirsch B, Horton T, Kahwash S, Levine J, Loken M, Brodersen L, Pollard J, Raimondi S, Kolb EA, Gamis A. Bortezomib with standard chemotherapy for children with acute myeloid leukemia does not improve treatment outcomes: a report from the Children's Oncology Group. Haematologica. 2020 Jul;105(7):1879-1886. doi: 10.3324/haematol.2019.220962. Epub 2020 Feb 6. PMID: 32029509; PMCID: PMC7327649.

Smith JL, Ries RE, Hylkema T, Alonzo TA, Gerbing RB, Santaguida MT, Eidenschink Brodersen L, Pardo L, Cummings CL, Loeb KR, Le Q, Imren S, Leonti AR, Gamis AS, Aplenc R, Kolb EA, Farrar JE, Triche TJ Jr, Nguyen C, Meerzaman D, Loken MR, Oehler VG, Bolouri H, Meshinchi S. Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study. Clin Cancer Res. 2020 Feb 1;26(3):726-737. doi: 10.1158/1078-0432.CCR-19-1800. Epub 2019 Nov 12. PMID: 31719049; PMCID: PMC7002196.

Hagiwara K, Ding L, Edmonson MN, Rice SV, Newman S, Easton J, Dai J, Meshinchi S, Ries RE, Rusch M, Zhang J. RNAIndel: discovering somatic coding indels from tumor RNA-Seq data. Bioinformatics. 2020 Mar 1;36(5):1382-1390. doi: 10.1093/bioinformatics/btz753. Erratum in: Bioinformatics. 2020 Aug 15;36(14):4231. PMID: 31593214; PMCID: PMC7523641.

Pardo LM, Voigt AP, Alonzo TA, Wilson ER, Gerbing RB, Paine DJ, Dai F, Menssen AJ, Raimondi SC, Hirsch BA, Gamis AS, Meshinchi S, Wells DA, Brodersen LE, Loken MR. Deciphering the Significance of CD56 Expression in Pediatric Acute Myeloid Leukemia: A Report from the Children's Oncology Group. Cytometry B Clin Cytom. 2020 Jan;98(1):52-56. doi: 10.1002/cyto.b.21829. Epub 2019 Jul 11. PMID: 31294507; PMCID: PMC7872511.

Iacobucci I, Wen J, Meggendorfer M, Choi JK, Shi L, Pounds SB, Carmichael CL, Masih KE, Morris SM, Lindsley RC, Janke LJ, Alexander TB, Song G, Qu C, Li Y, Payne-Turner D, Tomizawa D, Kiyokawa N, Valentine M, Valentine V, Basso G, Locatelli F, Enemark EJ, Kham SKY, Yeoh AEJ, Ma X, Zhou X, Sioson E, Rusch M, Ries RE, Stieglitz E, Hunger SP, Wei AH, To LB, Lewis ID, D'Andrea RJ, Kile BT, Brown AL, Scott HS, Hahn CN, Marlton P, Pei D, Cheng C, Loh ML, Ebert BL, Meshinchi S, Haferlach T, Mullighan CG. Genomic subtyping and therapeutic targeting of acute erythroleukemia. Nat Genet. 2019 Apr;51(4):694-704. doi: 10.1038/s41588-019-0375-1. Epub 2019 Mar 29. PMID: 30926971; PMCID: PMC6828160.

Alexander TB, Gu Z, Iacobucci I, Dickerson K, Choi JK, Xu B, Payne-Turner D, Yoshihara H, Loh ML, Horan J, Buldini B, Basso G, Elitzur S, de Haas V, Zwaan CM, Yeoh A, Reinhardt D, Tomizawa D, Kiyokawa N, Lammens T, De Moerloose B, Catchpoole D, Hori H, Moorman A, Moore AS, Hrusak O, Meshinchi S, Orgel E, Devidas M, Borowitz M, Wood B, Heerema NA, Carrol A, Yang YL, Smith MA, Davidsen TM, Hermida LC, Gesuwan P, Marra MA, Ma Y, Mungall AJ, Moore RA, Jones SJM, Valentine M, Janke LJ, Rubnitz JE, Pui CH, Ding L, Liu Y, Zhang J, Nichols KE, Downing JR, Cao X, Shi L, Pounds S, Newman S, Pei D, Guidry Auvil JM, Gerhard DS, Hunger SP, Inaba H, Mullighan CG. The genetic basis and cell of origin of mixed phenotype acute leukaemia. Nature. 2018 Oct;562(7727):373-379. doi: 10.1038/s41586-018-0436-0. Epub 2018 Sep 12. PMID: 30209392; PMCID: PMC6195459.

Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature. 2018 Mar 15;555(7696):371-376. doi: 10.1038/nature25795. Epub 2018 Feb 28. PMID: 29489755; PMCID: PMC5854542.

Bolouri H, Farrar JE, Triche T Jr, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2018 Jan;24(1):103-112. doi: 10.1038/nm.4439. Epub 2017 Dec 11. Erratum in: Nat Med. 2018 Apr 10;24(4):526. Erratum in: Nat Med. 2019 Mar;25(3):530. PMID: 29227476; PMCID: PMC5907936.

Lim EL, Trinh DL, Ries RE, Wang J, Gerbing RB, Ma Y, Topham J, Hughes M, Pleasance E, Mungall AJ, Moore R, Zhao Y, Aplenc R, Sung L, Kolb EA, Gamis A, Smith M, Gerhard DS, Alonzo TA, Meshinchi S, Marra MA. MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia. J Clin Oncol. 2017 Dec 10;35(35):3964-3977. doi: 10.1200/JCO.2017.74.7451. Epub 2017 Oct 25. Erratum in: J Clin Oncol. 2019 Jan 20;37(3):261. PMID: 29068783; PMCID: PMC5721230.